A moving bead biofilm reactor (MBBR) pilot plant was implemented as a partial nitrification process for pre-treatment of ammonium-rich liquors (676±195mgL-1), and studied for 479days under variations in hydraulic retention time. The main purpose of this work, was the study of dynamics abundance of total bacteria and single-cells nitrifying bacteria belonging to ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in biofilms and mixed liquor of the plant. The microbial monitoring was successfully achieved using fluorescence in situ hybridization combined with flocs disaggregation protocol as a useful microbial monitoring tool. A partial nitrification process with a N-NH4+ removal rate of about 38.6±14.8% was successfully achieved at 211days after start-up, with a clear dominance of AOB, which accounted for 11.3±17.0% of total bacterial cells compared with only 2.1±4.0% of NOB. The effluent obtained was subsequently supplied to an Anammox reactor for complete ammonium treatment.